gene expression

MicroRNAs are approximately 22 nucleotide long, noncoding RNAs that extensively mediate post-transcriptional gene expression.  They control cellular function by either degrading mRNAs or arresting their translation. MicroRNAs are involved in various critical functions, including the regulation of cellular differentiation, proliferation, angiogenesis, and apoptosis as well as (patho)physiologic conditions such as tumor progression/regression and cholesterol/glucose homeostasis. More recent studies show that microRNAs play a critical role in the response to cerebral, renal, and cardiovascular ischemia and have potential to act as biomarkers of these pathologies and even potential as a therapeutic agent to correct them. [click to continue…]

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EXPANDER (EXpression Analyzer and DisplayER) is a java-based tool for analysis of gene expression data[1].

  • data preprocessing and normalization
  • identification of differential genes
  • clustering and biclustering;
  • down-stream enrichment analyses of:
    • GO functional categories
    • TF binding sites in promoter regions
    • microRNA sites in 3′-UTRs
    • chromosomal locations
  • network-based analysis of the expression data

Expander (EXPression ANalyzer and DisplayER) is an integrated software platform for the analysis of gene expression data, which is freely available for academic use. It is designed to support all the stages of microarray data analysis, from raw data normalization to inference of transcriptional regulatory networks.

microRNA target predictions for Human, Mouse, Fly, and C. elegans

  1. Ulitsky I, Maron-Katz A, Shavit S, Sagir D, Linhart C, Elkon R, Tanay A, Sharan R, Shiloh Y, Shamir R. (2010) Expander: from expression microarrays to networks and functions. Nat Protoc 5(2), 303-22. [abstract]

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Researchers at the University of Texas Southwestern Medical Center, Dallas used microarray analysis to compare miRNA expression patterns of primary rat cardiomyocytes with different levels of myocardin-related transcription factors (MRTFs). MRTFs associate with serum response factor (SRF) to drive the expression of actin and other cytoskeletal protein genes. miR-145 and miR-143 were among the most strongly upregulated miRNAs in response to MRTFs, as revealed by microarray and confirmed by real-time PCR. Further study revealed that (SRF) controls the expression of miR-143 and miR-145 in smooth muscle cells, and these miRNAs, in turn, feed back to control the expression and function of multiple components of the cytoskeleton and the SRF regulatory network. This study adds to a growing body of work demonstrating the roles of miRNAs in regulating changes in gene expression and cell functions in response to injury and stress and further underscores their potential as therapeutic targets.

Xin M, Small EM, Sutherland LB, Qi X, McAnally J, Plato CF, Richardson JA, Bassel-Duby R, Olson EN.  (2009) MicroRNAs miR-143 and miR-145 modulate cytoskeletal dynamics and responsiveness of smooth muscle cells to injury.  Genes Dev 23(18),2166-178. [abstract]

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Researchers at Yale University have discovered that microRNAs play key roles in modulating the expression of genes involved in DNA damage recognition and repair.  They used a combination of microRNA microarrays (for identification of the miRs), bioinformatics (for prediction of the miR targets), and luciferase assays (for confirmation of the miR targets) to make their discoveries. (read more)

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